Regulatory domains controlling high intestinal vitamin D receptor gene expression are conserved in mouse and human

Abstract

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Genomic analysis of 1,25-dihydroxyvitamin D3 action in mouse intestine reveals compartment and segment-specific gene regulatory effects

“…The samples were prepared and analyzed as we have previously described ( 66 ). The ATAC-seq data are available in GEO as entry GSE134579.…”

“…Preparations were isolated as we have described previously (65). For ChIP-seq, after isolation, the crypts and villi were incubated in For ATAC-seq, samples were prepared as we have previously described (66). For RNA-seq, Trizol was quickly added and the villus or crypt pellet (20-50 μl pellet per sample) was dispersed by pipetting, the samples were flash frozen in liquid nitrogen, and the samples were stored at −80 C.…”

“…Finally, the samples were frozen on dry ice for 5 min before storage in the −80 C freezer. For ATAC-seq, samples were prepared as we have previously described (66). For RNAseq, Trizol was quickly added and the villus or crypt pellet was dispersed by pipetting, the samples were flash frozen in liquid nitrogen, and the samples were stored at −80 C. Sonicated lysate and the supernatant dilution buffer (1% of 100X ProteaseArrestTM for Mammalian [100X], 2% 1M Tris pH 8, 3% 5M NaCl, 0.4% 0.5 M EDTA, 5% of 20% Triton X, and MilliQ water) were mixed together at a ratio that would give a concentration of 0.22 to 0.24% SDS.…”